Curriculum vitæ

Magnus Nordborg

August 25, 2020

Education 2011–2016 “Developing maximum-resolution genotype- phenotype maps using whole-genome polymorphism 1985–1986 Swedish Defense Institute of Language / Uppsala data”, ERC-2010-AdG Proposal No 268962 – MAXMAP, University. Subjects: Russian language, Soviet & Eastern total amount C2,183,956 (PI). European Studies. 2014–2016 “Adaptation after bottlenecks”, DFG SPP 1529, 1986–1989 B.Sc., Lund University. Majors: and total amount for GMI component C200,000 (joint pro- Mathematics. Advisor: B. O. Bengtsson. posal with Neuffer, Osnabrück and Weigel, MPI). 1989–1994 Ph.D., Department of Biological Sciences, Stan- ford University. Advisor: M. W. Feldman. 1994–1997 Research Associate, Department of Ecology & Current support , University of Chicago. Advisors: J. Bergel- 2018–2020 “1001 Genomes+”, ERA-CAPS (FWF I 3684- son, B. Charlesworth & D. Charlesworth. B25), total amount for GMI component C355,542 (joint project with Paul Kersey, EBI, and Detlef Weigel, MPI). Current and Former Positions 2018–2023 “Elucidating the causes and consequences of the global pattern of epigenetic variation in Arabidopsis 1997–2000 Department of Genetics, Lund University: Re- thaliana”, ERC-2017-AdG 789037 – EPICLINES, total search Assistant Professor (“forskarassistent”). amount C2,498,468 (PI) 2000–2015 Molecular & Computational Biology, University of Southern California: Assistant Professor (2000–2004); Associate Professor (2004-2011); Research Associate Invited Presentations (last five years) Professor (2011–2015). 2015 2009– Gregor Mendel Institute, Austrian Academy of Sci- ences, Vienna: Scientific Director. 1. Cologne Spring Meeting (invited speaker), Cologne, Ger- many 2. 26th International Conference on Arabidopsis Research Awards & Honors (invited speaker), Paris, France. • Alfred P. Sloan Research Fellow (2003–2005). 3. Linnean Centre Network Meeting (keynote speaker), Up- • Fellow of the AAAS (elected 2010). psala, Sweden. • Corresponding Member of the Austrian Academy of Sci- 4. 11th International Congress of Molecular Biology ences (elected 2013). (keynote speaker), Iguazú Falls, Brazil. • EMBO Member (elected 2015). 5. Zürich-Basel Plant Sciences Center symposium “Unlock- ing the potential of diversity” (invited speaker), Zürich, Switzerland. Research Grants Past support (last five years) 2016 2011–2014 “Starting from scratch: adaptation to variable en- 1. Research Centre (departmental speaker), vironments after an extreme bottleneck”, DFG SPP 1529, Aarhus University, Aarhus, Denmark. total amount for GMI component C228,510 (joint pro- 2. Keystone Symposium “Plant Epigenetics: From Geno- posal with Weigel, MPI). type to Phenotype” (invited speaker), Taos, New Mexico. 2009–2014 “Integrated Genetic and Genomic Resources for a 3. Evolutionary Genetics and Genomics Symposium (in- Model System”, NIH 2 R01 RR016300-07, total amount vited speaker), Cambridge University, Cambridge. $2,841,375 (Investigator, minor fraction of budget [PI: 4. INRA Montpellier (departmental speaker), Montpellier, Freimer, UCLA]). France. 2009–2014 “Genomic analysis of the genotype-phenotype 5. Workshop on the biology of variation (invited partici- map”, NIH 2 P50 HG002790-06, total amount pant), Fondation des Treilles, Les Treilles, France. $12,201,508 (Investigator, major fraction of budget 6. EMBL-Wellcome Genome Campus Conference “Big [PI: Tavaré, USC]). Data in Biology and Health” (invited speaker), EMBL, 2011–2015 “Trans-national Infrastructure for Plant Genomic Heidelberg, . Science”, EC FP7 Proposal No 283496 – transPLANT, 7. Jacques Monod Conference “Evolutionary genomics and total amount for GMI component C321,830 (PI on sub- systems biology: bringing together theoretical and exper- award [PI: Kersey, EBI]). imental approaches” (speaker), Roscoff, France.

1 8. EMBO Members’ meeting (inaugural talk), EMBL, Hei- 8. 5th Conference on Plant Genome Evolution, Sitges, Spain delberg, Germany. (keynote speaker). 9. World Life Science Conference (invited speaker), Beijing, 9. SciLifeLab The Svedberg Seminar, Uppsala University, China. Uppsala, Sweden (invited speaker). 10. The 8th International Symposium on Plant Senescence 10. Workshop on Polygenic Scores and their Applications, (keynote speaker), Jeju Island, South Korea. New York Genome Center, New York, New York, USA 11. Robert Hill Seminar (invited speaker), University of (invited speaker). Sheffield, Sheffield, England. 2020 2017 1. 2020 Workshop on Population and Speciation Genomics, 1. Winter School on Plant Biotechnology and Environmen- Ceskýˇ Krumlov, Czechia (invited lecturer). tal Sustainability (lecturer), University of Verona, Alba di 2. 2020 Future Biotech Winter Retreat, Novosibirsk, Russia Canazei, Italy. (invited lecturer). 2. Gordon Research Conference “Ecological & Evolution- 3. “The Biology of Genomes”, Cold Spring Harbor Labo- ary Genomics”, Biddeford, Maine, USA. ratories, New York, USA (session chair [virtual due to 3. Mini-Symposium on Biomedical Big Data (invited Covid-19]). speaker), Guizhou Normal University, Guiyang, China. 4. “Virtual Black Forest Summer School: Plant Ecological 4. The Earlham Institute (invited speaker), Norwich, UK. Epigenetics” (keynote speaker). 5. EMBO-EMBL Symposium: The Mobile Genome (in- vited speaker), Heidelberg, Germany. Teaching Experience 6. Institute of Botany, Chinese Academy of Sciences (de- partmental speaker), Beijing, China. At Lund University 7. Agricultural Genomics 2017 (invited speaker), Huazhong 1997 Introductory Biology (lecturer). Agricultural University, Wuhan, China. 1997 Molecular Evolution (lecturer). 8. Department of Plant and Microbial Biology (departmental 1997–1999 Population Genetics (lecturer). speaker), University of Zürich, Zürich, Switzerland. 1998 Graduate course in genetic analysis (lecturer & orga- nizer). 2018 1. Lausanne Genomics Days (invited speaker), University of At University of Southern California Lausanne, Lausanne, Switzerland. BISC 313 “Population Genetics & Evolution” (co-taught 2. Third Bangalore School on Population Genetics and Evo- class, 2002–2003). lution (invited lecturer), International Centre for Theoret- BISC 325 “Genetics” (co-taught class, 2004, 2006, 2008). ical Sciences, Bangalore, India. BISC 403 “Advanced Molecular Genetics” (co-taught class, 3. 60th Annual Maize Genetics Conference (plenary 2000–2002). speaker), Saint-Malo, France. BISC 499 “Population Genetics & Molecular Evolution” (co- 4. II Joint Congress on Evolutionary Biology (speaker), taught class, 2004, 2008). Montpellier, France. BISC 542 “Seminar in Molecular Biology” (co-taught class, 5. 62nd Annual Congress of the Italian Society of Agricul- 2001–2003). tural Genetics (invited speaker), Verona, Italy. BISC 502a “Molecular Genetics & Biochemistry” (lecturer, 6. 41st Annual Meeting of the Molecular Biology Society of 2004). Japan, Yokohama, Japan (invited speaker). BISC 502b “Molecular Genetics & Biochemistry” (lecturer, 7. National Institute of Genetics, Mishima, Japan (depart- 2001–2002, 2006–2007). mental speaker). BISC 505 “Genomics & Molecular Genetics” (lecturer, 2001). 2019 BISC 510b Evolutionary Biology (lecturer, 2003–2007). BISC 549 Seminar in Integrative & Evolutionary Biology 1. Cambridge Epigenetics Club, Cambridge University, (lecturer, 2003–2007; organizer 2006). Cambridge, UK (invited speaker). MATH 577b “Computational Molecular Biology Labora- 2. Department of Bioscience, Aarhus University, Aarhus, tory” (lecturer, 2001–2002). Denmark (departmental speaker). 3. Bi-annual Tri-National Arabidopsis Conference, Zürich, Switzerland (invited speaker). Advisory Experience 4. Weizmann Institute, Rehovot, Israel (invited speaker). Former doctoral students 5. “At the forefront of plant research”, Centre de Recerca en Agrigenòmica (CRAG), Barcelona, Spain (invited 1. Jenny Hagenblad (1998–2002), Associate Professor, speaker). Linköping University 6. Department of Botany and Plant Sciences, University of 2. Badri Padhukasahasram (2002–2006), Postdoc, Cornell California, Riverside, California, USA (invited speaker). University 7. Salk Integrative Biology Symposium, Salk Institute, La 3. Chunlao Tang (2001–2006), Postdoc, CSHL. Jolla, California, USA (invited speaker). 4. Sung Kim (2002–2006), Postdoc, UCSF.

2 5. Keyan Zhao (2003–2007), Postdoc, Cornell University. 21. Matt Horton (2013–2015), Research Fellow, University of 6. Tina Hu (2002–2008), Postdoc, Princeton University. Zürich, Switzerland. 7. Yu Huang (2007–2010), Postdoc, UCLA. 22. Cheng-Ruei Lee (2014–2016), Assistant Professor, Na- 8. Liz Cooper (2005–2011), Postdoc, University of Miami. tional Taiwan University, Taipei, Taiwan. 9. Bjarni Vilhjálmsson (2007–2011), Postdoc, Harvard Uni- 23. Eriko Sasaki (2012–2020), Associate Professor, Kyushu versity. University, Kyushu, Japan. 10. Pei Zhang (2008–2014), Research staff, AstraZeneca. 11. Dazhe Meng (2008–2015), Programmer, Google. Current postdocs 12. Polina Novikova (2011–2016), Postdoc, Ghent Univer- sity. 1. Daniele Filiault (2010–). 13. Envel Kerdaffrec (2010–2017), Postdoc, University of 2. Benjamin Jaegle (2015–). Fribourg. 3. Pieter Clauw (2015–). 14. Fernando Rabanal (2010–2017), Postdoc, Max Planck In- 4. Alexandra Kornienko (2017–). stitute, Tübingen. 5. Tom Ellis (2018–). 6. Haijun Liu (2019–). 7. Yoav Voichek (2020–). Current doctoral students 1. Gökçe Aköz (2013–). Service 2. Robin Burns (2014–). Journals 3. Mayela Soto Jimenez (2015–). 4. Rahul Pisupati (2017–). • Editorial Board Member, Genome Biology (2017–). 5. Dejan Ðukic´ (2018–). • Editor, eLife (2014–). • Associate Editor, Plant Cell (2006–2008). • Associate Editor, Genetics (2004–2009). Former postdocs • Associate Editor, J. Mol. Evol. (2001–2007). • Regular reviewer for a number of journals, including 1. Hideki Innan (2001–2002), Associate Professor, Graduate Amer. J. Hum. Genet., Curr. Biol., Genetics, Genome University for Advanced Studies, Hayama. Biol., Genome Res., Nature, Nature Genetics, PNAS, 2. Yoko Ishino (2002–2003), Associate Professor, Hi- PLoS Biol., PLoS Genet., and Science. roshima University. • Member, Faculty of 1000, Section on Evolution- 3. Honggang Zheng (2001–2004), Group Leader, Cargill ary/Comparative Genetics (2004–2011). Specialty Canola Oils. • Head, Faculty of 1000, Section on Plant Genomes & Evo- 4. Noah Rosenberg (with Simon Tavaré, 2001–2005), Asso- lution (2011–2014). ciate Professor, Stanford University. 5. María José Aranzana (2002–2005), Postdoc, CSIC-IRTA, Barcelona. Funding agencies 6. Christopher Toomajian (2003–2008), Assistant Professor, • NSF Panel Member (2003). Kansas State University. • USDA-NRI Panel Member (2004). 7. Tom Turner (2009), Assistant Professor, UCSB. • Temporary Member, NIH Genome Study Section (2004). 8. Glenda Willems (2007–2009), Postdoc, MPI, Cologne. • ERC LS2 Starting Grant Panel (Member 2013-2017, 9. Marc Rehmsmaier (2009–2011), Group Leader, Compu- Chair 2019). tational Biology Unit, University of Bergen. • External reviewer of proposals for a number of agencies, 10. Susanna Atwell (2006–2011), Postdoc, UC Davis. including NSF, ERC, and the Wellcome Trust. 11. Vincent Segura (2010–2011), Researcher, INRA, Or- léans. 12. Alex Platt (2008–2011), Postdoc, UCLA. Policy workshops 13. Quan Long (2009–2012), Researcher, Mount Sinai • NSF Plant Cyber-infrastructure Workshop (2005). School of Medicine. • NRC workshop on the National Plant Genome Initiative, 14. Qingrun Zhang (2010–2012), Postdoc, Mount Sinai Washington, DC (2007). School of Medicine. • NSF workshop on the future of Arabidopsis research, 15. Marie-Stanislas Remigerau (2009–2013), Research Asso- Washington, DC (2008). ciate, USC. • EC-US Task Force on Biotechnology Research work- 16. Takashi Tsuchimatsu (2012–2014), Assistant Professor, shop “Genomes to Germplasm” (2013), INRA, Versailles, University of Tokyo. France. 17. Manu Dubin (2012–2015), Researcher, Bayer Crop- Science. Advisory boards and committees 18. Hannes Svardal (2012–2015), Research Professsor, U. Antwerpen, Antwerpen, Belgium. • External reviewing committee, Department of Evolution- 19. Ashley Farlow (2011–2015), Research Associate, U. Mel- ary Genetics, Max Planck Institute for Evolutionary An- bourne, Australia. thropology (2003). 20. Arthur Korte (2010–2015), Assistant Professor, Univer- • SAB, NSF project “Molecular and Functional Diversity sity of Würzburg, Germany. of the Maize Genome”, John Doebley, PI (2004–2006).

3 • Various committees at USC, including hiring, admissions, [4] Gökçe Aköz and Magnus Nordborg. The Aquilegia and the Provost’s advisory group on bioinformatics. genome reveals a origin of core eudicots. Genome • SAB, Umeå Plant Science Center (2011–2015). Biol., 20:256, 2019. • SAB, IAIC/Araport (2012–2016). [5] Matteo Togninalli, Ümit Seren, Jan A Freudenthal, • SAB, Arabidopsis Biological Resource Center (2012– J Grey Monroe, Dazhe Meng, Magnus Nordborg, Detlef 2015). Weigel, Karsten Borgwardt, Arthur Korte, and Do- • SAB, Cluster of Excellence on Plant Sciences (CEPLAS) minik G Grimm. AraPheno and the AraGWAS Catalog (2012–2018). 2020: a major database update including RNA-Seq and • SAB, EU FP7 project “RADIANT” (2013–2015). knockout mutation data for . Nu- • SAB, CAS-MPG Partner Institute for Computational Bi- cleic Acids Res., 2019. ology, Shanghai (2013–). • SAB, NSF Plant Genome Project “Biology of Rare Al- [6] Dorota Duszynska, Bjarni Vilhjálmsson, Rosa leles in Maize and Its Wild Relatives”, Ed Buckler, PI Castillo Bravo, Sandesh Swamidatta, Thomas E (2014–2017). Juenger, Mark T A Donoghue, Aurélie Comte, Magnus • SAB, NSF Plant Genome Project “PanAnd – Harnessing Nordborg, Timothy F Sharbel, Galina Brychkova, Pe- convergence and constraint to predict adaptations to abi- ter C McKeown, and Charles Spillane. Transgenerational otic stress for maize and sorghum”, Ed Buckler, PI (2020– effects of inter-ploidy cross direction on reproduction 2022). and F2 seed development of Arabidopsis thaliana F1 hybrid triploids. Plant Reprod., 32:275–289, 2019. Publications [7] Matthias Nagler, Thomas Nägele, Christian Gilli, Lena Fragner, Arthur Korte, Alexander Platzer, Ashley Far- Preprints low, Magnus Nordborg, and Wolfram Weckwerth. Eco- metabolomics and metabolic modelling: making the leap [1] Robin Burns, Terezie Mandáková, Tereziekova, Joanna from model systems in the lab to native populations in the Jagoda, Luz Mayela Soto-Jiménez, Chang Liu, Mar- field. Front. Plant Sci., 2018. tin A Lysak, Polina Yu. Novikova, and Magnus Nord- borg. Gradual evolution of allopolyploidy in Arabidopsis [8] Danièle L Filiault, Evangeline S Ballerini, Terezie suecica. bioRxiv, 264432, 25 August 2020. Mandáková, Gökçe Aköz, Nathan J Derieg, Jeremy Schmutz, Jerry Jenkins, Jane Grimwood, Shengqiang [2] Benjamin Brachi, Daniele Filiault, Paul Darme, Marine Shu, Richard D Hayes, Uffe Hellsten, Kerrie Barry, Le Mentec, Envel Kerdaffrec, Fernando Rabanal, Alison Juying Yan, Sirma Mihaltcheva, Miroslava Karafiátová, Anastasio, Matthew Box, Susan Duncan, Timothy Mor- Viktoria Nizhynska, Elena M Kramer, Martin A Lysak, ton, Polina Novikova, Matthew Perisin, Takashi Tsuchi- Scott A Hodges, and Magnus Nordborg. The Aquilegia matsu, Roderick Woolley, Man Yu, Caroline Dean, Mag- genome provides insight into adaptive radiation and re- nus Nordborg, Svante Holm, and Joy Bergelson. Plant veals an extraordinarily polymorphic chromosome with a genes influence microbial hubs that shape beneficial leaf unique history. Elife, 7, 2018. communities. bioRxiv, 181198, 26 August 2017. [9] Eriko Sasaki, Florian Frommlet, and Magnus Nordborg. GWAS with heterogeneous data: Estimating the frac- Research articles tion of phenotypic variation mediated by gene expression data. G3, 2018. [1] Ruben Gutzat, Klaus Rembart, Thomas Nussbaumer, [10] Envel Kerdaffrec and Magnus Nordborg. The maternal Falko Hofmann, Rahul Pisupati, Gabriele Bradamante, environment interacts with genetic variation in regulating Nina Daubel, Angelika Gaidora, Nicole Lettner, Mat- seed dormancy in Swedish Arabidopsis thaliana. PLoS tia Donà, Magnus Nordborg, Michael Nodine, and Or- One, 12:e0190242, 2017. trun Mittelsten Scheid. Arabidopsis shoot stem cells dis- play dynamic transcription and DNA methylation pat- [11] Rahul Pisupati, Ilka Reichardt, Ümit Seren, Pamela terns. EMBO J., e103667, 2020. Korte, Viktoria Nizhynska, Envel Kerdaffrec, Kristina Uzunova, Fernando A Rabanal, Daniele L Filiault, and [2] Takashi Tsuchimatsu, Hiroyuki Kakui, Misako Ya- Magnus Nordborg. Verification of arabidopsis stock col- mazaki, Cindy Marona, Hiroki Tsutsui, Afif Hedhly, lections using SNPmatch, a tool for genotyping high- Dazhe Meng, Yutaka Sato, Thomas Städler, Ueli Gross- plexed samples. Sci Data, 4:170184, 2017. niklaus, Masahiro M Kanaoka, Michael Lenhard, Mag- [12] Matteo Togninalli, Ümit Seren, Dazhe Meng, Joffrey nus Nordborg, and Kentaro K Shimizu. Adaptive reduc- Fitz, Magnus Nordborg, Detlef Weigel, Karsten Borg- tion of male gamete number in the selfing plant Arabidop- wardt, Arthur Korte, and Dominik Grimm. The AraG- sis thaliana. Nat. Commun., 11:2885, 2020. WAS Catalog: A curated and standardized Arabidopsis thaliana GWAS catalog. Nucleic Acids Res., 2017. [3] Eriko Sasaki, Taiji Kawakatsu, Joseph R. Ecker, and Magnus Nordborg. Common alleles of CMT2 and [13] Hannes Svardal, Anna Jasinska, Cristian Apetrei, Gio- NRPE1 are major determinants of CHH methylation vanni Coppola, Yu Huang, Christopher Schmitt, Beat- variation in Arabidopsis thaliana. PLoS Genet., rice Jacquelin, Michaela Müller-Trutwin, George We- 15:e1008492, 2019. instock, Paul Grobler, Richard Wilson, Trudy Turner,

4 Wesley Warren, Nelson Freimer, and Magnus Nordborg. Magnus Nordborg, and Karel Riha. Germline replica- Ancient hybridization and strong adaptation to viruses tions and somatic mutation accumulation are independent across African vervet monkey populations. Nat. Genet., of vegetative life span in Arabidopsis. Proc. Natl. Acad. 2017. Sci. USA, 2016.

[14] Takashi Tsuchimatsu, Pauline M Goubet, Sophie Gal- [23] Matthew W Horton, Glenda Willems, Eriko Sasaki, lina, Anne-Catherine Holl, Isabelle Fobis-Loisy, Hélène Maarten Koornneef, and Magnus Nordborg. The genetic Bergès, William Marande, Elisa Prat, Dazhe Meng, Quan architecture of freezing tolerance varies across the range Long, Alexander Platzer, Magnus Nordborg, Xavier of Arabidopsis thaliana. Plant Cell Environ., 2016. Vekemans, and Vincent Castric. Patterns of polymor- [24] Paul Fransz, Gabriella Linc, Cheng-Ruei Lee, phism at the self-incompatibility locus in 1,083 Ara- Saulo Alves Aflitos, Jesse R Lasky, Christopher Tooma- bidopsis thaliana genomes. Mol. Biol. Evol., 2017. jian, Ali Hoda, Janny Peters, Peter van Dam, Xianwen Ji, [15] Fernando A Rabanal, Terezie Mandáková, Luz M Soto- Mateusz Kuzak, Tom Gerats, Ingo Schubert, Korbinian Jiménez, Robert Greenhalgh, David L Parrott, Ste- Schneeberger, Vincent Colot, Rob Martienssen, Maarten fan Lutzmayer, Joshua G Steffen, Viktoria Nizhynska, Koornneef, Magnus Nordborg, Thomas E Juenger, Richard Mott, Martin A Lysak, Richard M Clark, and Hans de Jong, and M Eric Schranz. Molecular, genetic Magnus Nordborg. Epistatic and allelic interactions con- and evolutionary analysis of a paracentric inversion in trol expression of ribosomal RNA gene clusters in Ara- Arabidopsis thaliana. Plant J., 2016. bidopsis thaliana. Genome Biol., 18:75, 2017. [25] Polina Yu Novikova, Nora Hohmann, Viktoria Nizhyn- [16] Fernando A Rabanal, Viktoria Nizhynska, Terezie ska, Takashi Tsuchimatsu, Jamshaid Ali, Graham Muir, Mandáková, Polina Yu Novikova, Martin A Lysak, Alessia Guggisberg, Tim Paape, Karl Schmid, Olga M Richard Mott, and Magnus Nordborg. Unstable inheri- Fedorenko, Svante Holm, Torbjörn Säll, Christian Schlöt- tance of 45S rRNA genes in Arabidopsis thaliana. G3, terer, Karol Marhold, Alex Widmer, Jun Sese, Kentaro K 2017. Shimizu, Detlef Weigel, Ute Krämer, Marcus A Koch, and Magnus Nordborg. Sequencing of the genus Ara- [17] Martha Imprialou, André Kahles, Joshua G Steffen, Ed- bidopsis identifies a complex history of nonbifurcating ward J Osborne, Xiangchao Gan, Janne Lempe, Amar- speciation and abundant trans-specific polymorphism. jit Bhomra, Eric Belfield, Anne Visscher, Robert Green- Nat. Genet., 48:1077–1082, 2016. halgh, Nicholas P Harberd, Richard Goram, Jotun Hein, [26] Taiji Kawakatsu, Shao-Shan Carol Huang, Florian Jupe, Alexandre Robert-Seilaniantz, Jonathan Jones, Oliver Eriko Sasaki, Robert J Schmitz, Mark A Urich, Rosa Stegle, Paula Kover, Miltos Tsiantis, Magnus Nordborg, Castanon, Joseph R Nery, Cesar Barragan, Yupeng He, Gunnar Rätsch, Richard M Clark, and Richard Mott. Huaming Chen, Manu Dubin, Cheng-Ruei Lee, Cong- Genomic rearrangements in Arabidopsis considered as mao Wang, Felix Bemm, Claude Becker, Ryan O’Neil, quantitative traits. Genetics, 2017. Ronan C O’Malley, Danjuma X Quarless, The 1001 [18] Cheng-Ruei Lee, Hannes Svardal, Ashley Farlow, Moi- Genomes Consortium, Nicholas J. Schork, Detlef Weigel, ses Exposito-Alonso, Wei Ding, Polina Novikova, Car- Magnus Nordborg, and Joseph R Ecker. Epigenomic di- los Alonso-Blanco, Detlef Weigel, and Magnus Nord- versity in a global collection of Arabidopsis thaliana ac- borg. On the post-glacial spread of human commensal cessions. Cell, 166:492–505, 2016. Arabidopsis thaliana. Nat. Commun., 8:14458, 2017. [27] The 1001 Genomes Consortium. 1,135 genomes re- [19] Polina Yu Novikova, Takashi Tsuchimatsu, Samson Si- veal the global pattern of polymorphism in Arabidopsis mon, Viktoria Nizhynska, Viktor Voronin, Robin Burns, thaliana. Cell, 166:481—491, 2016. Olga M Fedorenko, Svante Holm, Torbjörn Säll, Elisa [28] Dazhe Meng, Manu Dubin, Pei Zhang, Edward J Os- Prat, William Marande, Vincent Castric, and Magnus borne, Oliver Stegle, Richard M Clark, and Magnus Nordborg. Genome sequencing reveals the origin of Nordborg. Limited contribution of DNA methyla- the allotetraploid Arabidopsis suecica. Mol. Biol. Evol., tion variation to expression regulation in Arabidopsis 2017. thaliana. PLoS Genet., 12:e1006141, 2016. [20] Envel Kerdaffrec, Danièle L Filiault, Arthur Korte, Eriko [29] Eriko Sasaki, Pei Zhang, Susanna Atwell, Dazhe Meng, Sasaki, Viktoria Nizhynska, Ümit Seren, and Magnus and Magnus Nordborg. “Missing” G x E variation con- Nordborg. Multiple alleles at a single locus control trols flowering time in Arabidopsis thaliana. PLOS seed dormancy in Swedish Arabidopsis. Elife, 5:e22502, Genet., 11:e1005597, 2015. 2016. [30] Ashley Farlow, H. Long, S. Arnoux, W. Sung, T. G. Doak, [21] Ümit Seren, Dominik Grimm, Joffrey Fitz, Detlef M. Nordborg, and M. Lynch. The spontaneous mutation Weigel, Magnus Nordborg, Karsten Borgwardt, and rate in the Fission Yeast Schizosaccharomyces pombe. Arthur Korte. AraPheno: A public database for Ara- Genetics, 2015. bidopsis thaliana phenotypes. Nucleic Acids Res., 2016. [31] Wesley C Warren, Anna J Jasinska, Raquel Garcia- [22] J Matthew Watson, Alexander Platzer, Anita Kazda, Svet- perez, Hannes Svardal, Chad Tomlinson, Mariano Roc- lana Akimcheva, Sona Valuchova, Viktoria Nizhynska, chi, Nicoletta Archidiacono, Oronzo Capozzi, Patrick

5 Minx, Michael J Montague, Kim Kyung, Ladeana W Ines Hellmann, and Magnus Nordborg. Massive genomic Hillier, Milinn Kremitzki, Tina Graves, Colby Chiang, variation and strong selection in Arabidopsis thaliana Jennifer Hughes, Nam Tran, Yu Wang, Vasily Ramen- lines from Sweden. Nature Genet., 45:884–890, 2013. sky, Oi-wa Choi, Yoon J Jung, Christopher A Schmitt, Nikoleta Juretic, Jessica Wasserscheid, Trudy R Turner, [39] Tanja Slotte, Khaled M Hazzouri, J Arvid Agren, Daniel Roger W Wiseman, Jennifer J Tuscher, Julie A Karl, Koenig, Florian Maumus, Ya-Long Guo, Kim Steige, Jöern E Schmitz, Roland Zahn, David H O’Connor, Adrian E Platts, Juan S Escobar, L Killian Newman, Wei Eugene Redmond, Alex Nisbett, Béatrice Jacquelin, Wang, Terezie Mandáková, Emilio Vello, Lisa M Smith, Michaela C Müller-Trutwin, Jason M Brenchley, Michel Stefan R Henz, Joshua Steffen, Shohei Takuno, Yaniv Dione, Martin Antonio, Gary P Schroth, Jay R Kaplan, Brandvain, Graham Coop, Peter Andolfatto, Tina T Hu, Matthew J Jorgensen, Gregg WC Thomas, Matthew W Mathieu Blanchette, Richard M Clark, Hadi Quesneville, Hahn, Brian Raney, Bronwen Aken, Juergen Schmitz, Magnus Nordborg, Brandon S Gaut, Martin A Lysak, Gennady Churakov, Angela Noll, Roscoe Stanyon, David Jerry Jenkins, Jane Grimwood, Jarrod Chapman, Si- Webb, Francoise Thibaud-Nissen, Magnus Nordborg, mon Prochnik, ShengQiang Shu, Daniel Rokhsar, Jeremy Tomas Marques-Bonet, Ken Dewar, George M Wein- Schmutz, Detlef Weigel, and Stephen I Wright. The stock, Richard K Wilson, and Nelson B Freimer. The Capsella rubella genome and the genomic consequences genome of the vervet (Chlorocebus aethiops sabaeus). of rapid mating system evolution. Nature Genet., 45:831– Genome Res., 4, 2015. 835, 2013. [32] Manu J. Dubin, Pei Zhang, Dazhe Meng, Marie-Stanislas [40] Marilyne Debieu, Chunlao Tang, Benjamin Stich, Tobias Remigereau, Edward J. Osborne, Francesco Paolo Sikosek, Sigi Effgen, Emily Josephs, Johanna Schmitt, Casale, Philipp Drewe, André Kahles, Geraldine Jean, Magnus Nordborg, Maarten Koornneef, and Juliette Bjarni Vilhjálmsson, Joanna Jagoda, Selen Irez, Viktor de Meaux. Co-variation between seed dormancy, growth Voronin, Qiang Song, Quan Long, Gunnar Rätsch, Oliver rate and flowering time changes with latitude in Ara- Stegle, Richard M. Clark, and Magnus Nordborg. DNA bidopsis thaliana. PLoS ONE, 8:e61075, 2013. methylation variation in Arabidopsis has a genetic basis [41] Quan Long, Qingrun Zhang, Bjarni J Vilhjálmsson, Petar and shows evidence of local adaptation. eLife, 2015. Forai, Umit Seren, and Magnus Nordborg. JAWAMix5: [33] N. Fulcher, A. Teubenbacher, E. Kerdaffrec, A. Farlow, an out-of-core HDF5-based java implementation of M. Nordborg, and K. Riha. Genetic architecture of natu- whole-genome association studies using mixed models. ral variation of telomere length in Arabidopsis thaliana. Bioinformatics, 29:1220–1222, 2013. Genetics, 2014. [42] Sandra Beleza, Nicholas A. Johnson, Sophie I. Can- [34] Matthew W Horton, Natacha Bodenhausen, Kathleen dille, Devin M. Absher, Marc A. Coram, Jailson Lopes, Beilsmith, Dazhe Meng, Brian D. Muegge, Sathish Sub- Joana Campos, Isabel Inês Araújo, Tovi M. Anderson, ramanian, M. Madlen Vetter, Bjarni J. Vilhjálmsson, Bjarni J. Vilhjálmsson, Magnus Nordborg, António Cor- Magnus Nordborg, Jeffrey I. Gordon, and Joy Bergelson. reia e Silva, Mark D. Shriver, Jorge Rocha, Gregory S. Genome-wide association study of Arabidopsis thaliana Barsh, and Hua Tang. Genetic architecture of skin and leaf microbial community. Nat. Commun., 5:5320, 2014. eye color in an African-European admixed population. PLoS Genet., 9:e1003372, 2013. [35] Christian D Huber, Magnus Nordborg, Joachim Hermis- son, and Ines Hellmann. Keeping it local: Evidence for [43] Ümit Seren, Bjarni J. Vilhjálmsson, Matthew W. Horton, positive selection in Swedish Arabidopsis thaliana. Mol. Dazhe Meng, Petar Forai, Yu S Huang, Quan Long, Vin- Biol. Evol., 31:3026–39, 2014. cent Segura, and Magnus Nordborg. GWAPP: A web application for genome-wide association mapping in A. [36] Peijin Li, Daniele Filiault, Mathew S. Box, Envel Kerdaf- thaliana. Plant Cell, 24:4793–4805, 2012. frec, Cock van Oosterhout, Amity M. 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[84] Chikako Shindo, María José Aranzana, Clare Lister, [96] Jenny Hagenblad and Magnus Nordborg. Sequence vari- Catherine Baxter, Colin Nicholls, Magnus Nordborg, and ation and haplotype structure surrounding the flower- Caroline Dean. Role of FRIGIDA and FLC in determin- ing time locus FRI in Arabidopsis thaliana. Genetics, ing variation in flowering time of Arabidopsis thaliana. 161:289–298, 2002. Plant Physiol., 138:1163–1173, 2005. [97] Magnus Nordborg, Justin O. Borevitz, Joy Bergelson, Charles C. Berry, Joanne Chory, Jenny Hagenblad, Mar- [85] Magnus Nordborg, Tina T. Hu, Yoko Ishino, Jinal tin Kreitman, Julin N. Maloof, Tina Noyes, Peter J. Jhaveri, Christopher Toomajian, Honggang Zheng, Er- Oefner, Eli A. Stahl, and Detlef Weigel. The extent of ica Bakker, Peter Calabrese, Jean Gladstone, Rana Goyal, linkage disequilibrium in Arabidopsis thaliana. Nature Mattias Jakobsson, Sung Kim, Yuri Morozov, Badri Pad- Genet., 30:190–193, 2002. hukasahasram, Vincent Plagnol, Noah A. Rosenberg, Chitiksha Shah, Jeffrey Wall, Jue Wang, Keyan Zhao, [98] Peter Donnelly, Magnus Nordborg, and Paul Joyce. Like- Theodore Kalbfleisch, Vincent Schultz, Martin Kreitman, lihoods and simulation methods for a class of non-neutral and Joy Bergelson. The pattern of polymorphism in Ara- population genetics models. Genetics, 159:853–867, bidopsis thaliana. PLoS Biol., 3:e196, 2005. 2001.

[86] Per Sjödin, Ingemar Kaj, Steven Krone, Martin Lascoux, [99] Magnus Nordborg. Linkage disequilibrium, gene trees, and Magnus Nordborg. On the meaning and existence of and selfing: An ancestral recombination graph with par- an effective population size. Genetics, 169:1061–1070, tial self-fertilization. Genetics, 154:923–929, 2000. 2005. [100] Magnus Nordborg. The coalescent with partial selfing [87] Ming Li, Magnus Nordborg, and Lei M. Li. Adjust qual- and balancing selection: An application of structured co- ity scores from alignment and improve sequencing accu- alescent processes. In Francoise Seillier-Moiseiwitsch, racy. Nucleic Acids Res., 32:5183–5191, 2004. editor, Statistics in Molecular Biology and Genetics, vol- ume 33 of IMS Lecture Notes-Monograph Series, pages [88] Carsten Wiuf, Keyan Zhao, Hideki Innan, and Magnus 56–76. Institute of Mathematical Statistics, Hayward, Nordborg. The probability and chromosomal extent of California, 1999. trans-specific polymorphism. Genetics, 168:2363–2372, 2004. [101] Magnus Nordborg and Joy Bergelson. The effect of seed and rosette cold treatment on germination and flowering [89] Jenny Hagenblad, Chunlao Tang, John Molitor, Jonathan time in some Arabidopsis thaliana (Brassicaceae) eco- Werner, Keyan Zhao, Honggang Zheng, Paul Marjoram, types. Am. J. Bot., 86(4):470–475, 1999. Detlef Weigel, and Magnus Nordborg. Haplotype struc- ture and phenotypic associations in the chromosomal re- [102] Magnus Nordborg. On the probability of Neanderthal gions surrounding two Arabidopsis thaliana flowering ancestry. Am. J. Hum. Genet., 63:1237–1240, 1998. time loci. Genetics, 168:1627–1638, 2004. [103] Peter Andolfatto and Magnus Nordborg. The effect of [90] Badri Padhukasahasram, Paul Marjoram, and Magnus gene conversion on intralocus associations. Genetics, Nordborg. Estimating the rate of gene conversion on hu- 148:1397–1399, 1998. man chromosome 21. Am. J. Hum. Genet., 75:386–397, [104] Brian Charlesworth, Magnus Nordborg, and Deborah 2004. Charlesworth. The effects of local selection, balanced polymorphism and background selection on equilibrium [91] Hideki Innan and Magnus Nordborg. The extent of link- patterns of genetic diversity in subdivided populations. age disequilibrium and haplotype sharing around a poly- Genet. Res., Camb., 70:155–174, 1997. morphic site. Genetics, 165:437–444, 2003. [105] Magnus Nordborg. Structured coalescent processes on [92] Hideki Innan, Badri Padhukasahasram, and Magnus different time scales. Genetics, 146:1501–1514, 1997. Nordborg. The pattern of polymorphism on human chro- mosome 21. Genome Res., 13:1158–1168, 2003. [106] Magnus Nordborg and Peter Donnelly. The coalescent process with selfing. Genetics, 146:1185–1195, 1997. [93] Magnus Nordborg and Hideki Innan. The genealogy of sequences containing multiple sites subject to strong se- [107] Magnus Nordborg, Brian Charlesworth, and Deborah lection in a subdivided population. Genetics, 163:1201– Charlesworth. The effect of recombination on back- 1213, 2003. ground selection. Genet. Res., Camb., 67:159–174, 1996.

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[2] Joy Bergelson, Edward S. Buckler, Joseph R. Ecker, [13] Justin O. Borevitz and Magnus Nordborg. The impact of Magnus Nordborg, and Detlef Weigel. A proposal re- genomics on the study of natural variation in Arabidopsis. garding best practices for validating the identity of ge- Plant Physiol., 132:718–725, 2003. netic stocks and the effects of genetic variants. Plant Cell, [14] Noah A. Rosenberg and Magnus Nordborg. Genealog- 28:606–609, 2016. ical trees, coalescent theory, and the analysis of genetic [3] Detlef Weigel and Magnus Nordborg. Population Ge- polymorphisms. Nature Rev. Genet., 3:380–390, 2002. nomics for Understanding Adaptation in Wild Plant [15] Magnus Nordborg and Hideki Innan. Molecular popula- Species. Annu. Rev. Genet., 49, 2015. tion genetics. Curr. Opin. Plant Biol., 5:69–73, 2002. [4] Nicholas J. Provart, José Alonso, Sarah M. Assmann, [16] Magnus Nordborg and Stephen M. Krone. Separation of Dominique Bergmann, Siobhan M. Brady, Jelena Brkl- time scales and convergence to the coalescent in struc- jacic, John Browse, Clint Chapple, Vincent Colot, Sean tured populations. In M. Slatkin and M. Veuille, editors, Cutler, Jeff Dangl, David Ehrhardt, Joanna D. Friesner, Modern Developments in Theoretical Population Genet- Wolf B. Frommer, Erich Grotewold, , ics: The Legacy of Gustave Malécot, pages 194–232. Ox- Jennifer Nemhauser, Magnus Nordborg, Craig Pikaard, ford University Press, Oxford, 2002. John Shanklin, Chris Somerville, Mark Stitt, Keiko U. Torii, Jamie Waese, Doris Wagner, and Peter McCourt. [17] Magnus Nordborg and Simon Tavaré. Linkage disequi- Tansley review 50 years of Arabidopsis research: high- librium: What history has to tell us. Trends Genet., lights and future directions. New Phytol., 2015. 18:83–90, 2002.

[5] Bjarni J. Vilhjálmsson and Magnus Nordborg. The na- [18] Magnus Nordborg. Coalescent theory. In D. J. Bald- ture of confounding in genome-wide association studies. ing, M. J. Bishop, and C. Cannings, editors, Handbook of Nature Rev. Genet., 14:1–2, 2012. Statistical Genetics, pages 179–212. John Wiley & Sons, Inc., Chichester, U.K., 2001. [6] Joost J. B. Keurentjes, Glenda Willems, Fred van Eeuwijk, Magnus Nordborg, and Maarten Koornneef. A [19] Magnus Nordborg. On detecting ancient admixture. In comparison of population types used for QTL mapping in Peter Donnelly and Robert A. Foley, editors, Genes, Fos- Arabidopsis thaliana. Plant Genet. Resour., 9:185–188, sils, and Behaviour: An Integrated Approach to Human 2011. Evolution, NATO Science Series, pages 123–136, Ams- terdam, 2001. IOS Press. [7] Magnus Nordborg and Detlef Weigel. Next-generation genetics in plants. Nature, 456:720–723, 2008. [20] Magnus Nordborg. Genealogical processes with general types of population structure. In Bulletin of the Interna- [8] Alan M. Jones, Joanne Chory, Jeffery L. Dangl, Mark Es- tional Statistical Institute, 52nd Session, volume LVIII, telle, Steven E. Jacobsen, Elliot M. Meyerowitz, Magnus pages 357–360, Helsinki, 1999.

10 [21] Magnus Nordborg. Deterministic Models of Natural Se- lection. PhD thesis, Stanford University, 1994.

11